I spent another 2.5 hours effin' around this evening.
I tried taking readings from different seating positions, and although there were differences, they weren't dramatic. Couldn't really say that one seat was much better than another.
Then I turned off YPAO and took some more readings. It was quite evident that it had been making a difference - it just couldn't work miracles.
So, I moved the mains outboard of the AT screen - to where you can see them in the first photo in this thread, before the grill cloth went up. I was then able to move the subs further apart, so that they are now at 1/4 distance from the sidewalls. I then ran YPAO again and you can see the difference it made. It ain't pretty, with or without YPAO, but I guess it's better with. I think I'll have better luck with this when I build a couple of subs and EQ them separately.